your hdd0 looks normal, i know it's a bit confusing at first but i'll try to explain
dev_hdd0/GAMES = your original game rip folder, this is where your backup managers copies the game. this folder isn't being checked and has no effect with launching game using this 3.55 method.
dev_hdd0/game = this is where game patches and demos install to, this is how the 3.55 method works, basically by tricking it as a demo launch.
what we're doing is installing the pkg with a modified eboot that points to /dev_hdd0/game/<GAMEID>
so after installing the pkg, you would transfer your original game rip's USRDIR contents to that /dev_hdd0/game/<GAMEID>/USRDIR ...never overwrite the eboot though